sovacool.dev - Kelly L. Sovacool

Contact: sovacool [at] umich.edu

View a PDF version of my CV: https://sovacool.dev/latex-cv/vitae_KLS.pdf

Education

Dates	Degree	Institution
2018-2023	PhD Bioinformatics	University of Michigan, Dept. of Computational Medicine and Bioinformatics Advisor: Patrick D. Schloss
2014-2018	BS Biology	University of Kentucky, Dept. of Biology Minor: Computer Science

Research Experience

Dates	Title	Lab	Projects
2023-present	Bioinformatics Software Engineer II	Frederick National Laboratory for Cancer Research	Develop and maintain open source bioinformatics workflows on the CCR Collaborative Bioinformatics Resource core team to support researchers at the National Cancer Institute.
2019-2023	Graduate Student Researcher	Schloss Lab, Dept. of Microbiology and Immunology, University of Michigan	- Developed, benchmarked, and maintained bioinformatics workflows and software packages in R & Python. - Built machine learning pipelines for human gut microbiome classification problems in colorectal cancer and C. difficile infection. - Published findings as reproducible papers in open access journals. - Collaborated with other scientists on microbiome projects. - Mentored junior lab members.
2018-2019	Rotation Student Researcher	Program in Biomedical Sciences, University of Michigan	Worked in several different bioinformatics labs to find the best mentorship fit.
2015-2018	Undergraduate Lab Assistant	Moseley Bioinformatics Lab, Dept. of Molecular and Cellular Biochemistry, University of Kentucky	- Developed a Python package for comparative genomics. Identified sets of orthologous and paralogous gene products to facilitate collinearity analysis and detection of gene duplication events.
2016-2018	BIO395 Independent Research Student	Weisrock Lab, Dept. of Biology, University of Kentucky	- Developed bash scripts and a SNP calling pipeline in Snakemake. - Population structure analysis of the Ambystoma tigrinum species complex. - Bayesian species delimitation of the Desmognathus fuscus species complex.
2015-2016	Undergraduate Lab Assistant	Jaromczyk Lab, Dept. of Computer Science, University of Kentucky	- Maintained the Epichloë festucae genome project database. - Analyzed RNA-seq data of Chenopodium quinoa and coffee ringspot virus.

Service

Dates	Title	Organization	Projects
2019-2022	Executive Committee Member: Open Source Technical Lead	Girls Who Code at U-M DCMB	- Plan, apply for funding, develop curriculum, and maintain resources to teach introductory Python programming & data science to young women+. - Facilitate collaborative development and maintenance of our open source teaching resources. - Organize our year-round Club and annual Data Science Summer Experience for high school women+.
2019-2022	Organizer and Maintainer	U-M Carpentries	- Co-lead development & maintenance of a curriculum for workshops teaching programming skills for reproducible research. - Maintain the website, develop curriculum, and organize workshops. - Collaborate with U-M Women in Science and Engineering to organize workshops for women+.
2021-2023	Mentor	Schloss Lab	Mentor an undergraduate student in building reproducible machine learning models to predict C. difficile infection severity from gut microbiome composition.
2021-2022	CoderSpaces co-host	U-M ISR Data Science Hub	Hold office hours at a weekly virtual help session for data science practitioners
2021	Peer reviewer		PLOS ONE (1)
2019-2021	Graduate Student Coordinator	U-M Data Analysis Networking Group	- Organize monthly meetings & a one-day symposium for researchers to sharpen their data analysis skills. - Apply for funding through a Rackham Interdisciplinary Workshop grant.
2009-present	Volunteer Sound Engineer	various churches and non-profit organizations	Mix FOH, monitors, recording, and live stream.

Teaching Experience

dates	Title	Organization	Event(s)
Mar 2019	Capstone Activity Leader	Females Excelling More in Math, Engineering, & the Sciences	Binary Numbers through Ozobots with GWC at U-M DCMB
Apr 2019	DNA Day Ambassador	Michigan DNA Day	Epigenetics & Scientific Journeys
2019-2022	Facilitator & Capstone Project Mentor	Girls Who Code at U-M DCMB	Weekly Club during the school year and week-long Summer Experience for high schoolers to learn Python for data science
Jan-Apr 2023	Graduate Student Instructor	BIOINF 576: Tool Development for Bioinformatics. Dept. of Computational Medicine & Bioinformatics	Develop curriculum and teach students the principles of software development in R & Python. Topics: software design, implementation, testing, documentation, issue tracking, peer review, and release.
Jun 2022	Instructor		Intro to R & RNA-Seq Workshop for ASM Microbe conference attendees
2012-2018	Tutor	freelance	for high school and college students in Biology, Calculus, Chemistry, Computer Science, and Bioinformatics.
2018-present	Workshop Instructor & Helper	U-M Carpentries	2-day Software Carpentry workshops teaching computational skills for reproducible research
Mar 2019	Workshop helper	Graduate Society of Black Engineers and Scientists	Data Visualization with Python Workshop

Continuing Education

Date	Title	Organization	Location
Jan 2020	Building Tidy Tools workshop at rstudio::conf	Rstudio, PBC	San Francisco, CA
Dec 2019	Winter School in Research Software Engineering	US Research Software Sustainability Institute	Seattle, WA
Jun 2019	Software Carpentry Instructor Training	The Carpentries	University of Michigan
May 2019	PyCon Education Summit & Conference	The Python Software Foundation	Cleveland, OH
Apr 2019	MICROBIOL 612.2	Riffomonas Minimal R Workshop	University of Michigan

Awards

Grants

Dates	Title	Institution	Amount
2022	Conference Travel Grant	Rackham Graduate School University of Michigan	$900
2020-2021	Rackham Interdisciplinary Workshop Grant	Rackham Graduate School University of Michigan	$500
2020	Conference Travel Grant	Rackham Graduate School University of Michigan	$800
2019-2020	Rackham Interdisciplinary Workshop Grant	Rackham Graduate School University of Michigan	$500
2019-2021	NIH T32 Bioinformatics Training Program Fellow	Bioinformatics Graduate Program University of Michigan
2017	Oswald Research & Creativity Award 2nd place in Biological Sciences	Office of Undergraduate Research University of Kentucky	$200
2017	Summer Research Grant	Office of Undergraduate Research University of Kentucky	$2,000
2014-2018	Presidential Scholarship	University of Kentucky	out-of-state full tuition

Honors

Dates	Title	Institution
2018	Graduated Cum Laude with Departmental Honors in Biology	University of Kentucky
2018	Biology Undergraduate Research Award Nominee	University of Kentucky
2014-2018	Lewis Honors College	University of Kentucky

Publications

Last updated: August 26, 2023

* Indicates co-first author.

Date	Article	Authors	badges
2023 Aug	Machine Learning Classification by Fitting Amplicon Sequences to Existing OTUs. mSphere	Armour CR, Sovacool KL, Close WL, Topçuoğlu BD, Wiens J, Schloss PD
2022 Jul	Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides Difficile Colonization in a Mouse Model of Colitis. mBio	Barron MR, Sovacool KL, Abernathy-Close L, Vendrov KC, Standke AK, Bergin IL, Schloss PD, Young VB
2022 Feb	OptiFit: An Improved Method for Fitting Amplicon Sequences to Existing OTUs. mSphere	Sovacool KL, Westcott SL, Mumphrey MB, Dotson GA, Schloss PD
2022 Jan	Developing and Deploying an Integrated Workshop Curriculum Teaching Computational Skills for Reproducible Research. JOSE	Lapp Z, Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Anderson JM, Lucas SK, Schloss PD
2021 Dec	Teaching Python for Data Science: Collaborative Development of a Modular & Interactive Curriculum. JOSE	Duda M, Sovacool KL, Farzaneh N, Nguyen VK, Haynes SE, Falk H, Furman KL, Walker LA, Diao R, Oneka M, Drotos AC, Woloshin A, Dotson GA, Kriebel A, Meng L, Thiede SN, Lapp Z, Wolford BN
2021 May	Mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. JOSS	Topçuoğlu BD, Lapp Z, *Sovacool KL, Snitkin E, Wiens J, Schloss PD
2021 Apr	Geography Is More Important than Life History in the Recent Diversification of the Tiger Salamander Complex. PNAS	Everson KM, Gray LN, Jones AG, Lawrence NM, Foley ME, Sovacool KL, Kratovil JD, Hotaling S, Hime PM, Storfer A, Parra-Olea G, Percino-Daniel R, Aguilar-Miguel X, O’Neill EM, Zambrano L, Shaffer HB, Weisrock DW
2020 Aug	Ten Simple Rules to Increase Computational Skills among Biologists with Code Clubs. PLoS Comput Biol	Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough J, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD
2016 Aug	Processing RNA-Seq Data of Plants Infected with Coffee Ringspot Virus. BMC Bioinform	Goodin MM, Farman M, Inocencio H, Jang C, Jaromczyk JW, Moore N, Sovacool KL

N = 9

Presentations

Talks

Date	Event	Title	Location
Nov 2022	Bioinformatics Student Research Hour	Predicting C. difficile infection severity from the taxonomic composition of the gut microbiome	University of Michigan
Feb 2022	Seminar for the KG Jebsen Center for Genetic Epidemiology	Intro to git & GitHub	(Virtual) Norwegian University of Science and Technology
Mar 2021	Bioinformatics Student Research Hour	OptiFit: a fast method for fitting amplicon sequences to existing OTUs	(Virtual) University of Michigan
Apr 2018	Systems Biology and Omics Integration Seminar	Developing a Global Homology Analysis for Comparative Genomics	University of Kentucky

Posters

Date	Event	Title	Location
Jun 2022	ASM Microbe	Predicting the severity of C. difficile infections from the taxonomic composition of the gut microbiome	Washington, DC
Jun 2020	ASM Microbe	OptiFit: a fast method for fitting amplicon sequences to existing OTUs	Virtual
Apr 2018	Showcase for Undergraduate Scholars	Developing a Global Homology Analysis for Comparative Genomics	University of Kentucky
Apr 2018	National Conference on Undergraduate Research	Developing a Global Homology Analysis for Comparative Genomics	University of Central Oklahoma
Apr 2016	Showcase for Undergraduate Scholars	Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus	University of Kentucky
Apr 2016	UT-KBRIN Bioinformatics Summit	Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus	Cadiz, KY
Apr 2015	Showcase for Undergraduate Scholars	The Effect of Meditation on Performance	University of Kentucky

Open Source Contributions

mikropml

machine learning

User-Friendly R Package for Supervised Machine Learning Pipelines

Co-author and maintainer

schtools

Schloss Lab tools for reproducible microbiome research

Co-author and maintainer

mikropml snakemake workflow

machine learning

Snakemake template for building reusable and scalable machine learning pipelines with mikropml

Co-author and maintainer

mothur

Command-line tool for processing microbial amplicon sequence data

mothur snakemake workflow

Snakemake template for reproducible microbial amplicon sequence analysis with mothur

U-M Software Carpentry

Intro to R, the Unix shell, and git for workshops on reproducible research.

Co-author and maintainer

Girls Who Code at U-M DCMB

Intro to Python for Data Science via Live-Coding for Girls Who Code clubs.

Co-author and maintainer

Code Clubs

Short coding tutorials for lab meetings

U-M DANG!

Reproducibility

repro-packs: Organizing projects for reproducibility and headache prevention.

Intro to R & RNA-seq

Workshop for 2022 ASM Microbe attendees

Skills

Languages & Tools

Research

supervised machine learning

data visualization

reproducible manuscripts

gut microbiome composition

amplicon sequence analysis

Software

package maintenance

test-driven development

continuous integration

collaboration & peer review

high performance computing